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NCMI Workshops: Cryo EM Image Processing

Workshop on Single Particle Reconstruction, Structural Variability and Modeling: Oct 30 - Nov 2, 2015

Presentation notes from the Workshop (some of these have not been uploaded yet)

Video of selected sessions Our primary video recording mechanism failed to record audio, so we unfortunately have only the EMAN and Modeling tutorials recorded

Tutorial PDFs

Tutorial Data You will also need all of the demonstration data, which we will use when going through the tutorials:

Completed Tutorial Projects (large files)

Software used at the workshop:

  • EMAN/SPARX 2.12 (or snapshot version released after Oct. 19, 2015) - (day 1 - 2) Required. Do not use an older version.

  • Relion 1.4 (optional, day 2-3) - The Relion session will largely be a demo. See comments below.

  • Chimera Daily Build Oct. 17 or later - For PDB viewing and Segger tutorial (day 4, specific version required)

  • Warning: we are aware of an issue with Gorgon on Ubuntu. Will remove this warning when resolved. Other Linux variants should be fine, now.
  • Gorgon - Gorgon Tutorial (day 4) Please install the appropriate binary AND

  • Phenix - (end of day 4) real-space refinement of models

  • LKH Solver - (day 4 - pathwalker), required only for the pathwalker tutorial, see below

  • OpenMPI and PyDusa (day 2-3) SPARX tutorial may also largely be a demo, see below

Cryo-EM Workshop at the National University of Singapore: July 9 - July 13, 2012


Structural & Computational Biomedical Informatics and Cryo-EM (UK): June 8 - June 12, 2009


Workshop on Single Particle Reconstruction, Map Interpretation and Visualization: Dec 10 - Dec 13, 2008


EMAN/Single Particle Tutorial: June 11, 2008


  • Talk1.pdf - Introduction to Single Particle Reconstruction in EMAN1 - Steve Ludtke

  • talk2-ctf.pdf - Introduction to Fourier Transforms and CTF Correction - Steve Ludtke

  • Demo1.pdf - Demo session containing walkthrough for EMAN1 DVD - Steve Ludtke

  • ffts.pdf - FFT's Part 1 (more detailed lecture) - Steve Ludtke

  • ffts2.pdf - FFT's Part 2 (more detailed lecture) - Steve Ludtke

Grand challenges for Nanomedicine and Nanobiology: Aug 27, 2007


CryoEM Structure Mining: June 17, 2007


CryoEM Training Workshop: June 8, 2007


Workshop on Single Particle Reconstruction and Visualization: Mar. 14, 2007


Introduction to Programming for Scientists Lecture Series: Jun. 12, 2006


Single Particle Reconstructions and Visualization EMAN Tutorial: Mar. 16 - Mar. 19, 2005


Workshop of the Center of Protein Folding Machinery: Dec. 4 - Dec. 5, 2004


National Center for Macromolecular Imaging Workshop on Single Particle Reconstructions and Visualization (& EMAN Tutorial): Dec. 11 - Dec. 15, 2002


Image Processing Workshop - Theory and Practice of Icosahedral Particle Reconstruction: Apr. 9, 2002